Markers + reference

Crateva

3 species · Capparaceae · Brassicales

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Species 3
Genome length 156–157 kb
Candidate markers 266
Primer pairs 95

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-AAA-rps16 LSC 966 0.0186 1.00 57.8 yes View details
trnR-AGA-atpA LSC 274 0.0370 0.92 66.1 yes View details
ycf3-trnS-UCC LSC 1088 0.0141 1.00 54.9 yes View details
petA-psbJ LSC 1102 0.0172 1.00 72.1 yes View details
trnP-CCA-psaJ LSC 380 0.0044 1.00 57.6 yes View details
psaJ-rpl33 LSC 443 0.0339 1.00 77.7 yes View details
rps8 LSC 405 0.0115 1.00 48.6 yes View details
ndhF SSC 2250 0.0111 1.00 48.9 yes View details
ndhF-rpl32 SSC 1048 0.0290 0.95 62.5 yes View details
rpl32-trnL-CUA SSC 570 0.0282 0.99 69.2 yes View details
ccsA-ndhD SSC 320 0.0446 0.98 67.3 yes View details
rpl14-rpl16 LSC 131 0.0308 0.99 67.5 yes View details
trnD-GAC-trnY-UAC LSC 464 0.0129 1.00 64.4 yes View details
ycf2-trnL-UUG IRb 966 0.0099 0.94 63.6 yes View details
trnL-UUG-ycf2 IRa 966 0.0099 0.94 63.6 yes View details
trnF-UUC-ndhJ LSC 490 0.0185 0.99 62.7 yes View details
ndhA SSC 2189 0.0091 1.00 62.6 yes View details
psaI-ycf4 LSC 427 0.0078 1.00 62.3 yes View details
trnS-AGC-trnG-GGA LSC 607 0.0121 1.00 61.9 yes View details
Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped.

Primer pairs

Showing the top 30 of 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-AAA-rps16_p1 trnK-AAA-rps16 CCATTTATTCGCTGGACCCA AAAAAGGCGCTCAACCTACA 1325–1340 1.000 82.0
trnK-AAA-rps16_p2 trnK-AAA-rps16 TGGAATCAGGGAAAGAGGGT AAAAAGGCGCTCAACCTACA 1356–1371 1.000 82.0
trnK-AAA-rps16_p3 trnK-AAA-rps16 CCATTTATTCGCTGGACCCA CCCAATGAGCCGTTTATCGA 1463–1478 1.000 81.7
trnK-AAA-rps16_p4 trnK-AAA-rps16 CCATTTATTCGCTGGACCCA TCCCAATGAGCCGTTTATCG 1464–1479 1.000 81.7
trnK-AAA-rps16_p5 trnK-AAA-rps16 TGGAATCAGGGAAAGAGGGT CCCAATGAGCCGTTTATCGA 1494–1509 1.000 81.6
trnS-AGC-trnG-GGA_p1 trnS-AGC-trnG-GGA CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 646–682 1.000 56.7
trnS-AGC-trnG-GGA_p2 trnS-AGC-trnG-GGA AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 645–681 1.000 56.7
trnS-AGC-trnG-GGA_p3 trnS-AGC-trnG-GGA CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 649–685 1.000 55.6
trnS-AGC-trnG-GGA_p4 trnS-AGC-trnG-GGA CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 648–684 1.000 55.6
trnS-AGC-trnG-GGA_p5 trnS-AGC-trnG-GGA AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 647–683 1.000 55.6
trnR-AGA-atpA_p1 trnR-AGA-atpA AGTGAAAAGCGTCCATTGTCT TCAAGAGCAACTGGAACGTT 381–398 1.000 74.7
trnR-AGA-atpA_p2 trnR-AGA-atpA AGTGAAAAGCGTCCATTGTCT TTCAAGAGCAACTGGAACGT 382–399 1.000 74.6
trnR-AGA-atpA_p3 trnR-AGA-atpA AGTGAAAAGCGTCCATTGTC TCAAGAGCAACTGGAACGTT 381–398 1.000 73.0
trnR-AGA-atpA_p4 trnR-AGA-atpA GTGAAAAGCGTCCATTGTCT TCAAGAGCAACTGGAACGTT 380–397 1.000 73.0
trnR-AGA-atpA_p5 trnR-AGA-atpA GTGAAAAGCGTCCATTGTCT TTCAAGAGCAACTGGAACGT 381–398 1.000 73.0
trnD-GAC-trnY-UAC_p1 trnD-GAC-trnY-UAC CGGTGCTCTGACCAATTGAA TGGCAATATGTCTACGCTGG 534–540 1.000 75.8
trnD-GAC-trnY-UAC_p2 trnD-GAC-trnY-UAC CGGTGCTCTGACCAATTGAA GGCAATATGTCTACGCTGGT 533–539 1.000 75.8
trnD-GAC-trnY-UAC_p3 trnD-GAC-trnY-UAC CGGTGCTCTGACCAATTGAA GGGGACGGACTGTAAATTCG 555–561 1.000 74.8
trnD-GAC-trnY-UAC_p4 trnD-GAC-trnY-UAC CGGTGCTCTGACCAATTGAA GGGACGGACTGTAAATTCGT 554–560 1.000 74.6
trnD-GAC-trnY-UAC_p5 trnD-GAC-trnY-UAC CGGTGCTCTGACCAATTGAA GATTCTTCCTGGGTCGATGC 588–594 1.000 74.2
ycf3-trnS-UCC_p1 ycf3-trnS-UCC AATTTCCTTCGGATTGAGCC TGTTACGCCTTGAACCACTC 1145–1153 1.000 65.3
ycf3-trnS-UCC_p2 ycf3-trnS-UCC AATTTCCTTCGGATTGAGCC ACGGAAAGAGAGGGATTCGA 1201–1209 1.000 65.0
ycf3-trnS-UCC_p3 ycf3-trnS-UCC AATTTCCTTCGGATTGAGCC ACAGTTCCAATGTTACGCCT 1155–1163 1.000 61.8
ycf3-trnS-UCC_p4 ycf3-trnS-UCC AATTTCCTTCGGATTGAGCC ATGTTACGCCTTGAACCACT 1146–1154 1.000 61.8
ycf3-trnS-UCC_p5 ycf3-trnS-UCC AATTTCCTTCGGATTGAGCC CCAATGTTACGCCTTGAACC 1149–1157 1.000 61.2
trnF-UUC-ndhJ_p1 trnF-UUC-ndhJ CCTCGTGTCACCAGTTCAAA CCCGAAAGTTGGATAGGGTG 601–606 1.000 83.0
trnF-UUC-ndhJ_p2 trnF-UUC-ndhJ CCTCGTGTCACCAGTTCAAA CCGAAAGTTGGATAGGGTGG 600–605 1.000 83.0
trnF-UUC-ndhJ_p3 trnF-UUC-ndhJ CCTCGTGTCACCAGTTCAAA ATCCACGGCTAAAACGGATC 627–632 1.000 82.7
trnF-UUC-ndhJ_p4 trnF-UUC-ndhJ ATGGTCGGGATAGCTCAGTT CCCGAAAGTTGGATAGGGTG 643–648 1.000 81.5
trnF-UUC-ndhJ_p5 trnF-UUC-ndhJ ATGGTCGGGATAGCTCAGTT CCGAAAGTTGGATAGGGTGG 642–647 1.000 81.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Crateva religiosa NC_073097.1 156531 View on NCBI ↗
Crateva tapia NC_049621.1 156962 View on NCBI ↗
Crateva unilocularis NC_050353.1 156417 View on NCBI ↗